BACKGROUND Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES. METHODS In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array. RESULTS The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities. CONCLUSIONS Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.

中文翻译：

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拷贝数变异和通过微阵列进行纯合性检测可在11,020个临床外显子病例中进行更精确的分子诊断。

背景技术外显子组测序（ES）已成功应用于单核苷酸变异（SNV）和小插入缺失的临床检测。但是，使用ES数据识别拷贝数变体（CNV）仍然具有挑战性。这项研究的目的是了解CNV的贡献并复制纯合子（ROH）的中性分析在ES病人的分子诊断中的作用。方法在11020名连续的ES患者队列中，对大部分编码SNP进行询问的Illumina SNP阵列分析进行了质量控制（QC）测量，并用于CNV / ROH检测。在这些患者中，在ES之前，同时或之后，在Baylor Genetics（BG）对3229例患者进行了临床染色体微阵列分析（CMA）。我们回顾性分析了CMA和QC阵列的发现。结果QC阵列可检测出约70％的CMA可检测到的致病性/可能致病性CNV（PCNV）。在11020例ES病例中，QC阵列在327例患者中鉴定出PCNV，在10例患者中鉴定出了与单亲二体性疾病（UPD）相关的ROH。在3229名同时在BG接受CMA的ES患者中，PCNV / UPD的总检出率为5.9％。并发ES和CMA中PCNV / UPD的检出率高于先前CMA的ES（7.2％对4.6％）。PCNV / UPD在分子诊断为CMA的ES病例中占17.4％（189/1089）的分子诊断，估计占所有分子诊断的ES病例的10.6％。在38例患者中发现了PCNV和SNV的双重诊断。在4例患者中检测到了与SNV呈杂合状态的影响单个隐性疾病基因的PCNV，在17例患者中检测到纯合和纯合缺失（主要是外显子缺失）。具有综合征表型和/或心血管异常的患者观察到较高的PCNV检测率。结论我们的临床基因组学研究表明，通过QC阵列或CMA检测PCNV / UPD可提高ES诊断率，为显性和隐性性状提供更精确的分子诊断，并能对双分子或多分子诊断的患者进行更完整的遗传诊断。使用具有疾病基因外显子覆盖的阵列同时进行ES和CMA，可以最有效地检测CNV和SNV，因此特别推荐用于对时间敏感的临床情况。具有综合征表型和/或心血管异常的患者观察到较高的PCNV检测率。结论我们的临床基因组学研究表明，通过QC阵列或CMA检测PCNV / UPD可提高ES诊断率，为显性和隐性性状提供更精确的分子诊断，并能对双分子或多分子诊断的患者进行更完整的遗传诊断。使用具有疾病基因外显子覆盖的阵列同时进行ES和CMA，可以最有效地检测CNV和SNV，因此特别推荐用于对时间敏感的临床情况。具有综合征表型和/或心血管异常的患者观察到较高的PCNV检测率。结论我们的临床基因组学研究表明，通过QC阵列或CMA检测PCNV / UPD可提高ES诊断率，为显性和隐性性状提供更精确的分子诊断，并能对双分子或多分子诊断的患者进行更完整的遗传诊断。使用具有疾病基因外显子覆盖的阵列同时进行ES和CMA，可以最有效地检测CNV和SNV，因此特别推荐用于对时间敏感的临床情况。为显性和隐性特征提供更精确的分子诊断，并为具有双重或多重分子诊断的患者提供更完整的遗传诊断。使用具有疾病基因外显子覆盖的阵列同时进行ES和CMA，可以最有效地检测CNV和SNV，因此特别推荐用于对时间敏感的临床情况。为显性和隐性特征提供更精确的分子诊断，并为具有双重或多重分子诊断的患者提供更完整的遗传诊断。使用具有疾病基因外显子覆盖的阵列同时进行ES和CMA，可以最有效地检测CNV和SNV，因此特别推荐用于对时间敏感的临床情况。